X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=89ddb28bfee495e7145be65740f860460bae44d6;hb=5d176c0f8049654ec3ae5a869c9ee3cecb991dc6;hp=a44e1f3d7e3e824a58e4b5c0eaa4d9c960b1deb8;hpb=ee4dd201fa4f2c4ede5b2e525c82cce0a37de363;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index a44e1f3..89ddb28 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -160,10 +160,12 @@ 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; }; A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */; }; A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A704E8A21106045D00870157 /* otuhierarchycommand.cpp */; }; + A70B00C8110885EB002F453A /* setdircommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B00C7110885EB002F453A /* setdircommand.cpp */; }; A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */; }; A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; }; - A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */; }; A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */; }; + A70F3FD01136E391004FDC52 /* mothurout.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70F3FCF1136E391004FDC52 /* mothurout.cpp */; }; + A71CB8A311354B9F00848EF7 /* parselistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB8A211354B9F00848EF7 /* parselistscommand.cpp */; }; A727E84A10D14568001A8432 /* readblast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727E84910D14568001A8432 /* readblast.cpp */; }; A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */; }; A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACCF10848E6100139801 /* hclustercommand.cpp */; }; @@ -179,6 +181,7 @@ A787821110A0AAE70086103D /* bayesian.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787821010A0AAE70086103D /* bayesian.cpp */; }; A78782AB10A1B1CB0086103D /* alignmentdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A78782AA10A1B1CB0086103D /* alignmentdb.cpp */; }; A787844510A1EBDD0086103D /* knn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787844410A1EBDD0086103D /* knn.cpp */; }; + A794201111107897003AECCD /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A794200F11107897003AECCD /* distancedb.cpp */; }; A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */; }; A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B0450D106CEEC90046FC83 /* slayer.cpp */; }; A7D176CF10F2558500159497 /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D176CE10F2558500159497 /* pcacommand.cpp */; }; @@ -187,6 +190,7 @@ A7E0AAB610D2886D00CF407B /* mgclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */; }; A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A782106913F900688F62 /* getsharedotucommand.cpp */; }; A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A823106A9AD700688F62 /* maligner.cpp */; }; + A7E8A22F1125939F0011D39C /* chimerarealigner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E8A22E1125939F0011D39C /* chimerarealigner.cpp */; }; A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */ = {isa = PBXBuildFile; fileRef = A7F5759610CEBC0600E20E47 /* libreadline.a */; }; EB1216880F619B83004A865F /* bergerparker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216870F619B83004A865F /* bergerparker.cpp */; }; EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216E40F61ACFB004A865F /* bstick.cpp */; }; @@ -535,14 +539,18 @@ A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = preclustercommand.cpp; sourceTree = SOURCE_ROOT; }; A704E8A11106045D00870157 /* otuhierarchycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuhierarchycommand.h; sourceTree = SOURCE_ROOT; }; A704E8A21106045D00870157 /* otuhierarchycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuhierarchycommand.cpp; sourceTree = SOURCE_ROOT; }; + A70B00C6110885EB002F453A /* setdircommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setdircommand.h; sourceTree = SOURCE_ROOT; }; + A70B00C7110885EB002F453A /* setdircommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setdircommand.cpp; sourceTree = SOURCE_ROOT; }; A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = SOURCE_ROOT; }; A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = SOURCE_ROOT; }; A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = SOURCE_ROOT; }; A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = SOURCE_ROOT; }; - A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = SOURCE_ROOT; }; - A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = SOURCE_ROOT; }; A70DECD71063D8B40057C03C /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = SOURCE_ROOT; }; A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = SOURCE_ROOT; }; + A70F3FCE1136E391004FDC52 /* mothurout.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurout.h; sourceTree = SOURCE_ROOT; }; + A70F3FCF1136E391004FDC52 /* mothurout.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurout.cpp; sourceTree = SOURCE_ROOT; }; + A71CB8A111354B9F00848EF7 /* parselistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistscommand.h; sourceTree = SOURCE_ROOT; }; + A71CB8A211354B9F00848EF7 /* parselistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistscommand.cpp; sourceTree = SOURCE_ROOT; }; A727E84810D14568001A8432 /* readblast.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readblast.h; sourceTree = SOURCE_ROOT; }; A727E84910D14568001A8432 /* readblast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readblast.cpp; sourceTree = SOURCE_ROOT; }; A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckrdp.h; sourceTree = SOURCE_ROOT; }; @@ -573,6 +581,8 @@ A78782AA10A1B1CB0086103D /* alignmentdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentdb.cpp; sourceTree = SOURCE_ROOT; }; A787844310A1EBDD0086103D /* knn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = knn.h; sourceTree = SOURCE_ROOT; }; A787844410A1EBDD0086103D /* knn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = knn.cpp; sourceTree = SOURCE_ROOT; }; + A794200F11107897003AECCD /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = SOURCE_ROOT; }; + A794201011107897003AECCD /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = SOURCE_ROOT; }; A7B04491106CC3E60046FC83 /* chimeraslayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayer.h; sourceTree = SOURCE_ROOT; }; A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayer.cpp; sourceTree = SOURCE_ROOT; }; A7B0450C106CEEC90046FC83 /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = SOURCE_ROOT; }; @@ -590,6 +600,8 @@ A7E4A782106913F900688F62 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = SOURCE_ROOT; }; A7E4A822106A9AD700688F62 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = SOURCE_ROOT; }; A7E4A823106A9AD700688F62 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = SOURCE_ROOT; }; + A7E8A22D1125939F0011D39C /* chimerarealigner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerarealigner.h; sourceTree = SOURCE_ROOT; }; + A7E8A22E1125939F0011D39C /* chimerarealigner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerarealigner.cpp; sourceTree = SOURCE_ROOT; }; A7F5759610CEBC0600E20E47 /* libreadline.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = libreadline.a; path = "../readline-6.0/libreadline.a"; sourceTree = SOURCE_ROOT; }; C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; }; @@ -676,6 +688,8 @@ 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */, 37E3ED800F4D9D0D00B5DF02 /* mothur.h */, 37D927EF0F21331F001D4494 /* mothur.cpp */, + A70F3FCE1136E391004FDC52 /* mothurout.h */, + A70F3FCF1136E391004FDC52 /* mothurout.cpp */, 373C691E0FC1C98600137ACD /* nast.hpp */, 373C691D0FC1C98600137ACD /* nast.cpp */, 373C692A0FC1C9EB00137ACD /* nastreport.hpp */, @@ -730,6 +744,8 @@ A75B887B104C16860083C454 /* ccode.cpp */, A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */, A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */, + A7E8A22D1125939F0011D39C /* chimerarealigner.h */, + A7E8A22E1125939F0011D39C /* chimerarealigner.cpp */, A7B04491106CC3E60046FC83 /* chimeraslayer.h */, A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */, 372A55531017922B00C5194B /* decalc.h */, @@ -914,8 +930,6 @@ A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */, A70B53A70F4CD7AD0064797E /* getlabelcommand.h */, A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */, - A70B53A90F4CD7AD0064797E /* getlinecommand.h */, - A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */, A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */, A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */, 370B88050F8A4EE4005AB382 /* getoturepcommand.h */, @@ -950,6 +964,8 @@ 375873F60F7D649C0040F377 /* nocommands.cpp */, A704E8A11106045D00870157 /* otuhierarchycommand.h */, A704E8A21106045D00870157 /* otuhierarchycommand.cpp */, + A71CB8A111354B9F00848EF7 /* parselistscommand.h */, + A71CB8A211354B9F00848EF7 /* parselistscommand.cpp */, 3792946E0F2E191800B9034A /* parsimonycommand.h */, 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, A7D176CD10F2558500159497 /* pcacommand.h */, @@ -980,6 +996,8 @@ 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */, 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */, 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */, + A70B00C6110885EB002F453A /* setdircommand.h */, + A70B00C7110885EB002F453A /* setdircommand.cpp */, 37D928270F21331F001D4494 /* sharedcommand.h */, 37D928260F21331F001D4494 /* sharedcommand.cpp */, 37D928470F21331F001D4494 /* summarycommand.h */, @@ -1016,6 +1034,8 @@ 37D927D40F21331F001D4494 /* database.hpp */, 37D927D30F21331F001D4494 /* database.cpp */, 37D927D50F21331F001D4494 /* datavector.hpp */, + A794201011107897003AECCD /* distancedb.hpp */, + A794200F11107897003AECCD /* distancedb.cpp */, 37D927DC0F21331F001D4494 /* fastamap.h */, 37D927DB0F21331F001D4494 /* fastamap.cpp */, 375873EA0F7D64520040F377 /* fullmatrix.h */, @@ -1226,7 +1246,6 @@ 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */, A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */, A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */, - A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */, EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */, EB9303F90F53517300E8EF26 /* geom.cpp in Sources */, EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */, @@ -1331,6 +1350,11 @@ A7D86C7D10FE09AB00865661 /* formatcolumn.cpp in Sources */, A7D86C8C10FE09FE00865661 /* formatphylip.cpp in Sources */, A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */, + A70B00C8110885EB002F453A /* setdircommand.cpp in Sources */, + A794201111107897003AECCD /* distancedb.cpp in Sources */, + A7E8A22F1125939F0011D39C /* chimerarealigner.cpp in Sources */, + A71CB8A311354B9F00848EF7 /* parselistscommand.cpp in Sources */, + A70F3FD01136E391004FDC52 /* mothurout.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1407,6 +1431,8 @@ GCC_WARN_UNUSED_PARAMETER = NO; GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; + LD_MAP_FILE_PATH = "$(TARGET_TEMP_DIR)/$(PRODUCT_NAME)-LinkMap-$(CURRENT_VARIANT)-$(CURRENT_ARCH).txt"; + LINK_WITH_STANDARD_LIBRARIES = YES; OTHER_CPLUSPLUSFLAGS = ( "-ansi", "-pedantic", @@ -1414,6 +1440,7 @@ "-lreadline", "-DUSE_READLINE", ); + OTHER_LDFLAGS = ""; PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; SYMROOT = /Users/johnwestcott/Desktop;